update to working version without ctrls data

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [0.2.4]
+
+# Fix
+- Fixed incompatibility when no control sample is provided
+- Fixed bug when relative paths are provided for test data
+
 # [0.2.3]
 
 ## Fix

README.md

@@ -1,6 +1,6 @@
 [![docker-release](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml/badge.svg)](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml)
 
-# RNAnue - 0.2.3
+# RNAnue - 0.2.4
 
 ## About
 RNAnue is a comprehensive analysis to detect RNA-RNA interactions from Direct-Duplex-Detection (DDD) data.

src/Data.cpp

@@ -32,7 +32,7 @@ Data::~Data() {
 
 void Data::preprocDataPrep() {
     // retrieve paths that contain the reads
-    fs::path ctrlsPath = fs::path(this->params["ctrls"].as<std::string>());
+    fs::path ctrlsPath = fs::path(params["ctrls"].as<std::string>());
     fs::path trtmsPath = fs::path(this->params["trtms"].as<std::string>());
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);
@@ -46,7 +46,10 @@ void Data::alignDataPrep() {
     } else {
         // make sure that data has been preprocessed (or at least selected)
         if(params["preproc"].as<std::bitset<1>>() == std::bitset<1>("1")) {
-            fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
+            fs::path ctrlsPath = "";
+            if(params["ctrls"].as<std::string>() != "") {
+                fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
+            }
             fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/trtms";
 
             /*
@@ -60,23 +63,32 @@ void Data::alignDataPrep() {
 }
 
 void Data::detectDataPrep() {
-    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
+    }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "align/trtms";
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);
     getCondition(groups);
 }
 
 void Data::clusteringDataPrep() {
-    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "detect/trtms";
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);
     getCondition(groups);
 }
 
 void Data::analysisDataPrep() {
-    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "detect/trtms";
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);

test/humanSE.cfg

@@ -46,7 +46,7 @@ clustdist = 0 # minimum distance between clusters
 
 ### ANALYSIS
 # specify the annotations of the organism of interest (optional)
-features =  gencode.v45.annotation.gff3 # GFF3 feature file
+features =  ref/gencode.v45.annotation.gff3 # GFF3 feature file
 
 # OUTPUT
 stats = 1 # produce a statistics of the libraries